If you haven't yet, go on a DNA collecting spree so that you have enough to purchase Upgrade 2 of the PK. This upgrade will allow you to pick up Tanks and Robots.
This is a fairly difficult mission. Start by jumping through the opening in the wall. Holobob yourself on the first person you see. Remember where you entered the Lab in the last mission? You have to do it again. Before you do, however, you're going to take care of a little groundwork which will help you out later. Holobob yourself and go to each of the four large Tesla Coils at the edges of the base. There are usually two EMP Mines near each one. Use your PK to destroy each one.
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When that is done, go near to the Lab door that you went through in the last mission. Target and use your PK on each of the two Majestic guards and toss them against the wall to kill them. This will not raise your alert and you can easily slip into the lab. Once inside the lab, locate the Scientist with the Pink Cloud above his head. Hypno him and tell him to "Deactivate the Gate". He'll run up the stairs and go the electric gate and deactivate it for you. You can do this yourself by blowing up the control panel, but if you do, you'll instantly have a full Alert Level. This is a much sneakier way.
Go through the now open doorway/gate and arm your Ion Detonator. Go forward and down the stairs. Destroy the two mutants using your Ion Detonator. Next, you have to destroy the two Research Data machines. These are the tape backup computers in the same room. After you destroy the two Data machines, two Majestic will come down the stairs. Kill them with your Disintegrator Ray. Note that this will cause a momentary Level 1 Alert Level, but it is nothing like have a full Alert Level.
You will be told that you have to destroy the four Tesla Coils in each corner of the Base. Fortunately, you already destroyed the EMP Mines near each one. If you purchased the Ion Detonator upgrade, you have a capacity of 10 rounds. This is good. Leave the lab, killing as you exit and go to each of the Tesla Coils. Each Coil will take 3 Ion Detonator shots and a few Disintegrator Rounds to blow up. This means that you can destroy 3 of them without having to find more ammo.
Finding ammo is fairly easy, especially if you are able to locate any of the Radioactive Cows. Find some green glowing cows and PK one of them into some nearby crates for some Ammo. Also, you can PK the radioactive cows into the Tesla Coils themselves if you like. You can do the same thing with Tanks as well, that is, PKing them and tossing them into the Tesla Coils. However, I found that you are under the most control if you simply stick to your Ion Detonator and simply find some Ammo along the way.
As you're destroying the Coils, you'll be under a lot of fire. You will probably die several times trying to get through this part of the mission. However, if you snuck into the lab earlier, you'll be in a much better Alert Level situation than if you storm into the lab. Stay on the move and if you see your Shield drop, take cover as fast as you can until your shield recharges.
Once all four Tesla Coils are destroyed, head to your Saucer. When you get to it, get in. If you need to clear the landing area of enemies, do so. Now you have to destroy the Majestic Base. Switch to your Sonic Boom and start destroying the marked targets. Be careful of you hull integrity. It shouldn't be much of an issue if you fly like a maniac, always moving left/right/up/down. When you destroy the central base, look for additional Sonic Boom ammo. You should have enough Sonic Boom ammo to destroy the entire base without have to resort to your Death Ray.
After this mission ends you have access to Upgrade 2 of your Disintegrator Ray for 1,000 DNA.
Before you start this mission, make sure that you have Upgrade 2 purchased for your PK. If you get exposed/caught at any time in this mission, re-Holobob as a soldier as quickly as possible and then run away until they forget about you. If any soldiers block the path at any time during this mission, first wait and see if they'll move on their own. Then, try to isolate them so as to not raise suspicion, and PK them out of the way.
It's time to destroy the Air Defenses and Gen. Armquist. Follow the path toward the Pink Diamond. On the way there, Holobob one of the soldiers. Go along the fence to the right and find the main gate. Wait for a truck to pull out and run in when the gate is open. As you approach the Pink Diamond, you'll be told that you need to Hypnotize the driver. There is a Constraint on this mission: No Police Alert. This won't be a problem.
Still disguised as a soldier, make sure that your Concentration Meter is full and then Hypno the drive and tell him to "Drive the Truck". After the cutscene, you'll have to Escort, follow, the truck. Stay disguised as a soldier. Run to the gate alongside the truck. Upon getting there, Hypno the soldier at the gate and make him "Sleep". Then, target the Control Switch and hit "Use" to open the gate.
The truck will next encounter another truck blocking the road. You can use your PK to move it. First, make sure your Concentration Meter is full and then hide behind a rock and use your PK to move the truck out of the way. You'll also have to PK the one Exploding Crate that is in the road. The soldiers in the area will be suspicious and may continue to block the road. If that's the case, just wait for the soldiers to wander to the side of the road so that your truck can pass.
Up next, there are some cows in the road. Use your PK to toss them out of the way...be sure to fill up on each cow before you toss it. After that you'll be blocked by some small boulders in the road. Put the soldier who is in the middle of the boulders to Sleep using your Hypno and then toss the boulders out of the way, being careful not to hit anybody with them.
Next, you'll encounter a mine field that you have to clear. Go ahead and de-Holobob. Arm your Zap-O-Matic and manually aim at each one and destroy it. Continue running forward taking out the 13 or 14 mines. You will be spotted by a few soldiers during this time. It's fine, kill them if you need to. Otherwise, just clear the mines, re-Holobob as a soldier, and then run back to your truck and PK the roadblocks out of the way. Escort the truck to the gates.
Finally, you have to get the truck through the gates. The best way to do this is from the inside. Run left along the fence until you are in a back corner. De-Holobob and fly over the fence. Land and immediately find a soldier to Holobob. Now inside, be careful of Majestic. Run to the gate (remember, the Pink Diamond is the truck) and target the Control Switch and hit "Use". The gates will open. You'll then need to PK each of the three road blocks. There will still be soldiers in the way. Just wait for them to disperse. When the truck finally comes to a stop, you'll be told that you need to defend the truck (which carries the bomb). You'll see a T-Minus countdown clock. You have to defend the truck until it reaches 1:00. Use your Disintegrator Ray to kill anybody marked with Pink Light.
Once the clock reaches 1:00 you need to get the heck out of there; out of the blast zone. Head towards your Blue Home Icon (your ship), fly over the fence and run left along the ridge/fence until the mission ends. I had about 0:18 left and I took my time, so you shouldn't have any problem.
After you complete this mission, Upgrade 2 of your Sonic Boom is now available in the Lab.
At the start of this mission you gain the Quantum Deconstructor for your Saucer. Use it the same way you use other Saucer weapons. It does some serious damage. And thank goodness, because your mission is to destroy Santa Modesta. This is an all out survival mission. The more buildings you destroy, the more ammo and shields you'll uncover, thus feeding this frenzy. Your main goal is to stay alive.
Use the Death Ray to destroy any artillery that is firing on you, including tanks. It helps to clear out some of the enemies first and then use your Sonic Boom and Quantum Deconstructor on the Pink marked buildings.
You need 1500 DNA in order to unlock the next mission.
You need 1500 DNA to unlock this mission. If you've already purchased all of the upgrades except for Upgrade 2 - Sonic Boom, go ahead and purchase this upgrade before the mission begins.
You've been shot down and are now a captive. From the start, PK the scientist out of the way and then target and PK the switch on the control panel. You'll get the option to "Use". Do so and your cage will de-electrify. Use your PK on the two Majestic guards to kill them.
Exit the building and you'll be told to retrieve your gun. It is marked by a Pink Diamond on the radar. Head there. When you get to it, walk into the gun. During the cutscene, you'll realize that you don't have a power cell for the gun. It is marked and is not far away from you. It's the green floating item. Grab it. Now, you have all of your guns. You'll need ammo. PK any crates marked "UFO" to reveal ammo.
Next, you have to scan three workers to find info on your ship's location. The workers are marked with Pink Clouds above their heads. Holobob then find and scan each one. Be wary of Majestic. After you scan all three, you'll have to talk to the Barge Driver. You need to do this disguised, however. If you run up the Barge Driver as an Alien, he'll run off of the ship and you'll have to find another way off of the island, namely by finding you Jet Pack.
If you approach the Barge Driver disguised (I was a soldier), he'll tell you that he won't take you anywhere without proper clearance. If you've been scanning people on the way to the barge, you probably overheard that the password is "Marilyn". "Start Conversation" with the Barge Driver and choose "Marilyn". He'll take you to the island.
If you did manage to scare away the Barge Driver, then go and find your Jet Pack which is marked. Once you get it, you'll have to fly to the island. To do so, you'll have to fly from blue-lighted buoy to buoy until you reach the island.
I highly recommend taking the Barge because it won't raise your Alert Level. Either way, once you're on the island, you have to get to your saucer. Make sure you are Holobobbed. You shouldn't have to worry about Majestic until you get near the Saucer. You'll see your Saucer hanging from a crane. Go up to the yellow sawhorses blocking the entrance and you'll be told by Pox that the humans are moving the ship. You must prevent this.
You'll see two Majestic near a UFO crate. PK the crate into the Majestic to knock them down. Then run along the left side of the area, past the trailer, until you see an orange dock worker with a Pink Cloud above his head. Hypno him and make him "Free the Saucer". After the cutscene, go up to the Saucer. Pox will talk to you. Afterwards, your Jet Pack will be under the ship (if you didn't already get it).
Now that you have the Jet Pack, you have to collect six power cells. They are all marked. Four of them are on a cargo ship. This will require you to fly from barge to barge, and then up to a ship. On the ship use your radar to locate the four Power Cells. The other two power cells are in the same general area as your Saucer. Once you collect all six, head to your Saucer. Of course, you'll have to clear the area of any enemies before you can board. Do so and then board your Saucer.
Once flying, you'll be told to destroy the base. This isn't too hard. I used the Sonic Boom exclusively.
To unlock the next mission you need to collect 2,000 DNA. This mission also unlocks a new B-Movie, "Furon Down". A new upgrade is available, Upgrade 1 for the Quantum Deconstructor.
You need to make your way to the White House. Holobob the first person you see and go to the Pink Diamond. Upon getting there, you'll see a scientist come out with a Pink Cloud over his head. Scan him and then follow him as he runs away. Keep scanning him to keep your Concentration Meter full. Keep doing this until you hear Pox tell you that you have received the code, "Blue Rider".
You have to head to Armquist's HQ and convince a soldier to let you in. Head there by crossing the bridge; avoid any Majestic on the way there and don't lose your disguise (I was a civilian woman). When you get to the gate you'll be able to talk to the soldier at the gate. Use "Blue Rider" as the password and you'll gain access.
Now inside, don't get caught. Head to the helicopter area where you will see a cutscene with Armquist and the mysterious mask guy. At this point, your recon work is done. You need to get back to your Saucer, but it is being stolen by humans. You have 3:00 to get back to your saucer. Don't worry about staying disguised, although it does help. Run back to the saucer, clear the area so you can board it. As soon as you can, do so and the mission will end.
After this mission ends you'll have access to Upgrade 2 of your Ion Detonator.
Before you start this mission, purchase Upgrade 2 for you Ion Detonator.
From the start you'll see a black Majestic sedan driving by you. It is marked with a Pink Light. Quickly Holobob the first person you see and then follow the car. Avoid any majestic on the way there. When you arrive you'll be told that you have to Hypnotize and put to Sleep the Navy Warlord. Facing the hangar entrance, go to the left of the hangar (follow your radar) and find the Navy Warlord walking around with a Pink Cloud over his head.
The Navy Warlord is being followed by a Robot and a Majestic. Get in front of the Navy Warlord and Hypno him, then Holobob him from a distance. If the people around are giving you trouble, you can PK them out of the way without raising any awareness. Once you are disguised as the Navy Officer, go to the Pink Light inside the hangar.
Next, you'll have to answer a series of questions. First, "Blame Rowdy Kids". Then ask, "Did You Catch the Assassin?". This will make the other Commanders leave and make Armquist look like a fool. After the cutscene you'll have to face off with Robot Armquist. You have 10 shots with your Ion Detonator. Launch a shot at his chest and then explode it. Repeat for all 10 of your shots. This will take Armquist down to just a sliver of health. Then, use your Disintegrator Ray to finish him off. None of his attacks are anything to worry about. Just strafe left/right and you should be fine.
After this mission ends, Upgrade 3 for your PK will be available. It is 3,000 DNA, but is well worth it as it doubles your concentration reserve.
Once again, return to the White House to check for a motorcade of black vehicles outside of it. When you near, the motorcade will drive away. You need to follow it to the Press Conference. Follow it until it stops. Egad! It's an ambush. Time to blow up anything with a Pink Light above it. I used the Ion Detonator and a little PK on one of the Robots.
After that is cleaned up, you are told to assassinate the President. He is marked by a Pink Light/Diamond. Holobob somebody that is around and then head to the President. You are timed (1:40) but shouldn't have any problem getting there. The President is on a raised platform. Simply shoot him with whatever weapon you choose.
Next, you have to get to your Saucer where there are Majestic agents trying to destroy it. Run there as fast as you can, you are timed again (1:45), and then destroy anybody who is near your Saucer. Get into your Saucer to end the mission.
Completing this mission will give you access to Upgrade 3 of your Zap-O-Matic
Now that the President is dead, you have to kill Senators as they file into the Capitol Building. Run to the Pink Light and hang out on the Capitol Stairs. Shoot anybody coming up the stairs. Note the count on the right of your screen. This count indicates the number of Senators that have gotten by you and entered the building. Don't let it build up to 20 or the mission will end. Keep killing anyone running up the stairs until you are told to go to the North entrance. Follow your radar to the Pink Light. From this position, continue to kill, and then when you are told to return to the previous position, do so. Soon, some Robots will enter the area, PK or Ion Detonate them and continue to kill Senators. If there is not activity (no Senators are coming), then go forward to the cars and see if any Senators are stuck behind cars.
After this mission, you'll have access to Upgrade 3 of your Disintegrator Ray.
Your goal here is simple: Destroy every Tesla Coil in town. After destroying the first one, you'll be told to eliminate the Scientists as well. Run around, using your radar to find the Scientists and the Tesla Coils. If you see a Scientist with a Pink Cloud over his head, Hypno him and have him "Overload the Tesla Coil". This will take out several coils at one time. Continue running around like a wild alien destroying any coils using your Ion Detonator.
You now have access to Upgrade 2 of your Quantum Deconstructor.
Go forward to the Capitol. Here you will meet Silhouette. Egad! He's a She! And, she introduces you to Roboprez, the 50ft super weapon. When the cutscene ends, run to your Saucer and get in. Destroying Roboprez isn't too hard as there is lots of Ammo and Repair Pods in the area. Go after him first with any Quantum Deconstructors you have and then rail him with your Sonic Boom. If you're Health Meter gets low, fly around and find a grouping of Repair Pods and Ammo. Anytime you have Quantum Deconstructor ammo, use it. Try to aim for the chest of Roboprez as it seems to do more damage than at the feet. Also, don't get too close to him or he'll use his green laser on you.
After you defeat Roboprez, you'll be told to land at the Octagon. Fly to the Pink Diamond on your radar, bing sure to keep an eye out for any Repair Pods. After you land, you'll have to defeat Silhouette!
You can kill Silhouette the easy way or the hard way. The hard way is to jump over the fence and fight her within the confines of the fence. The easy way is to stay outside of the fence and shoot her through the fence. First, note her Health Meter is below you Concentration Meter. Second, note that when she turns pink, she is healing and cannot take damage, so don't waste ammo on her when she's in this state. Third, in order to get her to come to the fence, you do need to fly over the fence, locate her, and then have her chase you.
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Once you get her against the fence, you need to be outside of the fence. Then, lay into her with your Disintegrator Ray (I had it upgraded to Upgrade 2). Keep doing this until you run out of ammo. When that happens, change to your Ion Detonator (also at Upgrade 2), step away from the fence a tad so it won't hurt you, and then launch a round at the fence near where she is standing and have it explode at the fence. Repeat this until you're out of ammo. At this point, you can switch to your Zap-O-Matic, but it is worth it to go ahead and jump into the battle area and gather some Ammo from the various ruins, or by breaking open the crates marked "UFO". Once you are resupplied, go back outside the fence and repeat the process. Again, if you run out of ammo a second time, you may just want to use your Zap-O-Matic and slowly take away her health.
When she dies you'll get a nice movie for the ending. Congrats! Now go find all of those Probes!
For completing the Story Missions you'll earn a new B-Movie, a new Furonigami item, and a new Propaganda item.